crbs/cws

CRBS Workflow Service -- Is a REST Service to enable execution of Kepler Workflows via Panfish

cws's Issues

Enable workspacefile deletion

Deletion should be logical and optionally real. A workspace file can only be deleted if its not part of any task as input or output.

Add taskinputworkspacefiles entity

this entity maps Task to Workspace files for input. This will be needed for deletion

Enable task deletion

Task deletion should be logically and optionally real. Tasks who's output workspace file isn't being used can be deleted. In addition if its a real delete the taskinputworkspace entries also need to be removed.

modify jobCmd.sh to send notification email when job starts and completes

jobCmd.sh should send an email when the job starts and completes.

Enable Grouping of parameters

Investigate a way to group a set of parameters (initially checkbox parameters) onto a single line with a single query such as seen with "Example 4:" checkbox in the url below.

http://www.alpacajs.org/examples/components/fields/checkbox-field.html

Perhaps in kepler we can use an annotation box and put parameters in that box with a display label

need to support custom view of runnable workflows on a per user basis

Need to enable a way so each user only sees a subset of workflows they are allowed to run. This can also be restricted to certain versions of workflows as well.

Enable system so only latest version of workflow is shown

Need to somehow disable older versions of workflows so only the latest is displayed

modify jobCmd.sh to run kepler in a polling mode

The jobCmd.sh script which runs kepler should run kepler in the background and in a loop periodically check for job completion. While doing this the script should also look for the workflow.status file and if updated it should call cws jar with the file to update the service with changes.

Automatically add CWS_ special parameters if not included in Job and are in Workflow

When a job is added to the service the service should add any CWS_ special variables that are listed as part of the workflow to the parameter list. This is needed so the code involved in creation of the job script will add those variables to the command line.

enable workflow deletion

Only allowed if no tasks have run the workflow. deletion can be logical and real. Also if real, the blob file in google cloud also needs to be removed.

Add deploy infrastructure for cws jar

There needs to be a way to bundle cws.jar with a script and create a tarball for distribution. Ideally a user should be able to make a change to the pom, deploy the service to their Google App Engine account and then grab a tarball for the cws jar which they can then install somewhere to set up the service daemon.

Enable radio button

Enable radio button:
http://www.alpacajs.org/examples/components/fields/radio-field.html

--size and --md5 values are not being set when calling command line program with --updatepath flag

--size and --md5 values are not being set when calling command line program with --updatepath flag

Looking at the code the WorkspaceFileDAO needs updatePath method to be modified to support
size and md5. In addition the REST call to update the WorkspaceFile also needs to be adjusted
to consume size and md5 as query parameters

Do not allow creation of jobs without owner field being set

A job was inserted into the system where the owner is null. This job will never run cause the daemon running the jobs require the owner to be set. The code needs to be modified to set the owner properly or to verify owner is set to a correct value

Complete implementation of workspace registration via jobCmd.sh script

Complete the logic in jobCmd.sh to register the Job's output into the workspace when a job starts and to set its path when a job completes. The code should use the user's login and authentication tokens in the jobCmd.sh file instead of the same admin ones.

Complete custom "user" page in GAE admin page

There is a users.html page that is deployed into the Google App Engine administration page which is designed to let admins add, update, and remove users. This page needs to be completed.